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Yorodumi- PDB-6f34: Crystal structure of a bacterial cationic amino acid transporter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f34 | ||||||
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Title | Crystal structure of a bacterial cationic amino acid transporter (CAT) homologue bound to Arginine. | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Amino Acid Transporter / SLC7 | ||||||
Function / homology | Function and homology information cellular response to magnesium starvation / transmembrane transporter activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Jungnickel, K.E.J. / Newstead, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for amino acid transport by the CAT family of SLC7 transporters. Authors: Jungnickel, K.E.J. / Parker, J.L. / Newstead, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f34.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f34.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 6f34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f34_validation.pdf.gz | 990.9 KB | Display | wwPDB validaton report |
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Full document | 6f34_full_validation.pdf.gz | 994.6 KB | Display | |
Data in XML | 6f34_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 6f34_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f34 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f34 | HTTPS FTP |
-Related structure data
Related structure data | 5oqtSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 49658.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK0930, ApcT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5L1G5 |
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#2: Protein/peptide | Mass: 2965.577 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yneM, b4599, JW1527.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A5A616 |
-Non-polymers , 4 types, 78 molecules
#3: Chemical | ChemComp-ARG / | ||
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#4: Chemical | ChemComp-CLR / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.99 % |
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Crystal grow | Temperature: 292 K / Method: lipidic cubic phase / pH: 4 Details: 28-34 % PEG 400, 0.1 M sodium acetate pH 4.0 and 0.1 M potassium fluoride, containing 10 mM of the amino acid ligand. |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 30, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.13→64.63 Å / Num. obs: 13951 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 94.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.074 / Rrim(I) all: 0.188 / Net I/σ(I): 5.5 / Num. measured all: 89902 / Scaling rejects: 84 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OQT Resolution: 3.13→50.926 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.42 Å2 / Biso mean: 99.082 Å2 / Biso min: 55.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.13→50.926 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -12.3337 Å / Origin y: -1.9101 Å / Origin z: 25.4411 Å
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Refinement TLS group |
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